I was trying to understand Eli’s What’s so special about neck and found myself getting snarled by definitions.
I wrote, _ "One thing that confuses me: contrasting “neck” with “string” _ and, unfortunately, the reply was to consult the Glossary/Dictionary from which I’d just come!
Neck (neck area): “The neck area is where the beginning and the end of the RNA sequence ends in a string.”
Sorry, doesn’t help me a bit.
There’s something I’m missing … probably a single simple factoid; the contradistinction neck / string refuses to come clear for me.
FWIW, entries with “string” in them. NB: 2 entries for “String”; no mention of"stalk".
Arm – almost the same as stack, stem and string, but meaning the whole arm in a design, eg. two strings and the bulge between them.
End loops - Mat coined the term Ends for a loop at the ending of a string.
Leg - Eterna slang for string, stem. Can mean whole leg consisting of more stems.
Neck (neckarea) The neck area is where the beginning and the end of the RNA sequence ends in a string. Thanks to Ding for coining Neck.
My definition is: The neck area, is a string, that behave quite different to the other strings. The neck area allows more repetitative patterns than in the rest of the strings. Also the neck is allowed to have very high total negative energy or very low total negative energy, compared with the energy distribution in the rest of the designs. I found out that there tend to be a relative even energy distribution, in the highscoring designs. The neckarea is the only area in the design that is allowed to break it
Stack – same as stem and string - basepairs lined up beside each other
Stem – same as leg, stack and string. The scientists calls them stem most of the time
Strand – nucleotides in a row – like strawberries on a straw. It takes two strands to make a string.
String - A string is two lines of nucleotides or a line of base pairs on a row. String - from one junction to another. A string stops as soon as a bulge or loop begins.
String - same as leg, stack and string. The scientists calls them stem most of the time.